In the first few years of his episcopate, Gordon made a determined, unsuccessful effort to stamp out the growth of Presbyterianism. In 1549 the Scottish provincial council convened to reform the Scottish church.[2] Bishop Gordon was, arguably, part of the problem, as he had fathered eight children by an unmarried woman named Janet Knowles whom he supported with episcopal revenues.[2] In 1560 the Scottish Church broke its ties to Rome, banned Mass and established an independent Scottish Church.[2] Gordon was not an enthusiastic supporter of the latter and after the return of Mary, Queen of Scots - a Roman Catholic - to Scotland and her takeover of the kingdom, he assumed a low profile and the Queen issued a decree of protection to the University of Aberdeen, of which Gordon was chancellor; Gordon's nephew, moreover, was the staunchly Catholic George Gordon, 4th Earl of Huntly.[2]